Large rifle primers are ever so slightly longer and if seated in a larger pistol primer pocket they stick out like they aren't fully seated. If used in some semiautos there is the possibility of a slam-fire!

added;
According to SAAMI, the depths for small pistol, small rifle, and large pistol primer pockets are .118" to .122", while large rifle primer pocket depths are .128" to .132". Small pistol and small rifle primers have the same diameter (.175") while large rifle and large pistol primers are also the same (.210").